docs: def align(self, input_path, output_path, directions, pipeline, 
                filter_minimum):
          '''align - Takes input path to fasta of unaligned reads, aligns them to
          a HMM, and returns the aligned reads in the output path
  
          Parameters
          ----------
          input_path : str
          output_path : str
          reverse_direction : dict
              A dictionary of read names, with the entries being the complement
              strand of the read (True = forward, False = reverse)
          pipeline : str
              Either "P" or "D" corresponding to the protein and nucleotide (DNA)
              pipelines, respectively.
  
  
          Returns
          -------
          N/A - output alignment path known.
          '''
  
          # HMMalign the forward reads, and reverse complement reads.
          with tempfile.NamedTemporaryFile(prefix='for_conv_file', suffix='.fa') as fwd_fh:
              fwd_conv_file = fwd_fh.name
              with tempfile.NamedTemporaryFile(prefix='rev_conv_file', suffix='.fa') as rev_fh:
                  rev_conv_file = rev_fh.name
                  alignments = self._hmmalign(
                      input_path,
                      directions,
                      pipeline,
                      fwd_conv_file,
                      rev_conv_file)
                  alignment_result = self.alignment_correcter(alignments,
                                                              output_path,
                                                              filter_minimum)
                  return alignment_result